tbuckley/cabot-search huggingface dataset:
Prognostic impact of fluorescent lymphography on gastric cancer
Authors: Sung Hyun Park, Ki-Yoon Kim, Minah Cho, Yoo Min Kim, Hyoung-Il Kim, Woo Jin Hyung
Journal: International Journal of Surgery (2023)

Fluorescent lymphography-guided lymphadenectomy (FL) for gastric cancer is gaining popularity. However, its impact on prognosis is not known. This study aimed to assess the prognostic impact of FL in gastric cancer patients.This study retrospectively analyzed 5678 gastric cancer patients who underwent gastrectomy from 2013 to 2017. The survival was compared between the FLFL group and the conventional lymphadenectomy (non-FL group) using 1:1 propensity score matching after exclusion. Patients in the FL group underwent gastrectomy with systematic lymphadenectomy after endoscopic peritumoral injection of indocyanine green the day before surgery.After propensity score matching, the FL and non-FL groups each had 1064 patients with similar demographic and clinicopathological characteristics. All matched variables had a standardized mean difference under 0.1. The FL group showed a significantly higher number of retrieved lymph nodes (56.2±20.1) than the non-FL group (46.2±18.2, P <0.001). The FL group also had more stage III patients ( P= 0.044) than the non-FL group. The FL group demonstrated higher overall survival ( P= 0.038) and relapse-free survival ( P= 0.036) in stage III compared with the non-FL group. However, no significant differences in overall and relapse-free survival were observed between the two groups for stages I ( P= 0.420 and P= 0.120, respectively) and II ( P= 0.200 and P= 0.280, respectively).FL demonstrated a higher survival in stage III gastric cancer patients by the more accurate staging resulting from larger lymph node retrieval. Thus, given its potential to improve prognostication by enhancing staging accuracy, it is recommended as an option to consider the use of FL in clinical practice.
Inflammatory biomarkers and nanotechnology: new insights in pancreatic cancer early detection
Authors: Damiano Caputo, Erica Quagliarini, Alessandro Coppola, Vincenzo La Vaccara, Benedetta Marmiroli, Barbara Sartori, Giulio Caracciolo, Daniela Pozzi
Journal: International Journal of Surgery (2023)

Poor prognosis of pancreatic ductal adenocarcinoma (PDAC) is mainly due to the lack of effective early-stage detection strategies. Even though the link between inflammation and PDAC has been demonstrated and inflammatory biomarkers proved their efficacy in predicting several tumours, to date they have a role only in assessing PDAC prognosis. Recently, the studies of interactions between nanosystems and easily collectable biological fluids, alone or coupled with standard laboratory tests, have proven useful in facilitating PDAC diagnosis. Notably, tests based on magnetic levitation (MagLev) of biocoronated nanosystems have demonstrated high diagnostic accuracy in compliance with the criteria stated by WHO. Herein, the author developed a synergistic analysis that combines a user-friendly MagLev-based approach and common inflammatory biomarkers for discriminating PDAC subjects from healthy ones.Plasma samples from 24 PDAC subjects and 22 non-oncological patients have been collected and let to interact with graphene oxide nanosheets.Biomolecular corona formed around graphene oxide nanosheets have been immersed in a Maglev platform to study the levitation profiles.Inflammatory biomarkers such as neutrophil-to-lymphocyte ratio (NLR), derived-NLR (dNLR), and platelet to lymphocyte ratio have been calculated and combined with results obtained by the MagLev platform.MagLev profiles resulted significantly different between non-oncological patients and PDAC and allowed to identify a MagLev fingerprint for PDAC. Four inflammatory markers were significantly higher in PDAC subjects: neutrophils ( P =0.04), NLR ( P =4.7 ×10 -6 ), dNLR ( P =2.7 ×10 -5 ), and platelet to lymphocyte ratio ( P =0.002). Lymphocytes were appreciably lower in PDACs ( P =2.6 ×10 -6 ).Combining the MagLev fingerprint with dNLR and NLR returned global discrimination accuracy for PDAC of 95.7% and 91.3%, respectively.The multiplexed approach discriminated PDAC patients from healthy volunteers in up to 95% of cases. If further confirmed in larger-cohort studies, this approach may be used for PDAC detection.
scTour: a deep learning architecture for robust inference and accurate prediction of cellular dynamics
Authors: Qian Li
Journal: Genome biology (2023)

Abstract Despite the continued efforts, a batch-insensitive tool that can both infer and predict the developmental dynamics using single-cell genomics is lacking. Here, I present scTour, a novel deep learning architecture to perform robust inference and accurate prediction of cellular dynamics with minimal influence from batch effects. For inference, scTour simultaneously estimates the developmental pseudotime, delineates the vector field, and maps the transcriptomic latent space under a single, integrated framework. For prediction, scTour precisely reconstructs the underlying dynamics of unseen cellular states or a new independent dataset. scTour’s functionalities are demonstrated in a variety of biological processes from 19 datasets.
In vitro and in vivo study on fine-grained Mg–Zn–RE–Zr alloy as a biodegradeable orthopedic implant produced by friction stir processing
Authors: Vasanth C. Shunmugasamy, Marwa AbdelGawad, Muhammad Umar Sohail, Talal Ibrahim, Talha Khan, Thomas Daniel Seers, Bilal Mansoor
Journal: Bioactive Materials (2023)

Magnesium alloys containing biocompatible components show tremendous promise for applications as temporary biomedical devices. However, to ensure their safe use as biodegradeable implants, it is essential to control their corrosion rates. In concentrated Mg alloys, a microgalvanic coupling between the α-Mg matrix and secondary precipitates exists which results in increased corrosion rate. To address this challenge, we engineered the microstructure of a biodegradable Mg-Zn-RE-Zr alloy by friction stir processing (FSP), improving its corrosion resistance and mechanical properties simultaneously. The FS processed alloy with refined grains and broken and uniformly distributed secondary precipitates showed a relatively uniform corrosion morphology accompanied with the formation of a stable passive layer on the alloy surface. In vivo corrosion evaluation of the processed alloy in a small animal model showed that the material was well-tolerated with no signs of inflammation or harmful by-products. Remarkably, the processed alloy supported bone until it healed till eight weeks with a low in vivo corrosion rate of 0.7 mm/year. Moreover, we analyzed blood and histology of the critical organs such as liver and kidney, which showed normal functionality and consistent ion and enzyme levels, throughout the 12-week study period. These results demonstrate that the processed Mg-Zn-RE-Zr alloy offers promising potential for osseointegration in bone tissue healing while also exhibiting controlled biodegradability due to its engineered microstructure. The results from the present study will have profound benefit for bone fracture management, particularly in pediatric and elderly patients.
The top 10 research priorities for pancreatitis: findings from a James Lind Alliance priority setting partnership
Authors: Vikramjit Mitra, Stacey Munnelly, Tassos Grammatikopoulos, Damian Mole, Andrew Hopper, Barbara Ryan, Mary Phillips, Maryrose Tarpey, John Leeds
Journal: The Lancet. Gastroenterology & hepatology (2023)
Disparities in diabetes prevalence and management by race and ethnicity in the USA: defining a path forward
Authors: Saria Hassan, Unjali P Gujral, Rakale C Quarells, Elizabeth C Rhodes, Megha K Shah, Jane Obi, Wei-Hsuan Lee, Luwi Shamambo, Mary Beth Weber, K M Venkat Narayan
Journal: The Lancet Diabetes & Endocrinology (2023)
Randomized-controlled trials are methodologically inappropriate in adolescent transgender healthcare
Authors: Florence Ashley, Diana M. Tordoff, Johanna Olson-Kennedy, Arjee J. Restar
Journal: International Journal of Transgender Health (2023)

Despite multiple rigorous observational studies documenting the association between positive mental health outcomes and access to puberty blockers, hormone therapy, and transition-related surgeries among adolescents, some jurisdictions have banned or are attempting to ban gender-affirming medical interventions for minors due to an absence of randomized-controlled trials (RCTs) proving their mental health benefits.
Gastrin attenuates sepsis-induced myocardial dysfunction by down-regulation of TLR4 expression in macrophages
Authors: Dandong Fang, Yu Li, Bo He, Daqian Gu, Mingming Zhang, Jingwen Guo, Hongmei Ren, Xinyue Li, Ziyue Zhang, Ming Tang, Xingbing Li, Donghai Yang, Chunmei Xu, Yijie Hu, Hongyong Wang, Pedro A. Jose, Yu Han, Chunyu Zeng
Journal: Acta Pharmaceutica Sinica B (2023)

Myocardial dysfunction is the most serious complication of sepsis. Sepsis-induced myocardial dysfunction (SMD) is often associated with gastrointestinal dysfunction, but its pathophysiological significance remains unclear. The present study found that patients with SMD had higher plasma gastrin concentrations than those without SMD. In mice, knockdown of the gastrin receptor, cholecystokinin B receptor (Cckbr), aggravated lipopolysaccharide (LPS)-induced cardiac dysfunction and increased inflammation in the heart, whereas the intravenous administration of gastrin ameliorated SMD and cardiac injury. Macrophage infiltration plays a significant role in SMD because depletion of macrophages by the intravenous injection of clodronate liposomes, 48 h prior to LPS administration, alleviated LPS-induced cardiac injury in Cckbr-deficient mice. The intravenous injection of bone marrow macrophages (BMMs) overexpressing Cckbr reduced LPS-induced myocardial dysfunction. Furthermore, gastrin treatment inhibited toll-like receptor 4 (TLR4) expression through the peroxisome proliferator-activated receptor α (PPAR-α) signaling pathway in BMMs. Thus, our findings provide insights into the mechanism of the protective role of gastrin/CCKBR in SMD, which could be used to develop new treatment modalities for SMD.
Associations between social health factors, cognitive activity and neurostructural markers for brain health – A systematic literature review and meta-analysis
Authors: Lukas A. Duffner, Nathan R. DeJong, Jacobus F.A. Jansen, Walter H. Backes, Marjolein de Vugt, Kay Deckers, Sebastian Köhler
Journal: Ageing Research Reviews (2023)

Social health factors (e.g., social activities or social support) and cognitive activity engagement have been associated with dementia risk, but their neural substrates have not been well established. This systematic review and meta-analysis summarizes the available evidence regarding the association between these factors and cerebral macro- and micro-structure. A comprehensive literature search was conducted in various databases, following predefined criteria. Heterogeneity, risk of publication bias and overall certainty of evidence were assessed using standardized scales and, whenever appropriate, random effects meta-analysis was conducted. Of 6715 identified articles, 43 were included. Overall, consistency of findings was low and methodological heterogeneity high for all outcomes. However, in some studies cognitive and social activities were positively associated with total brain, global and cortical grey matter and hippocampal volume as well as white matter microstructural integrity. Furthermore, structural social network characteristics (e.g., social network size) were associated with regional grey matter volumes, while functional social network characteristics (e.g., social support) were additionally associated with total brain volume. Meta-analyses revealed small but significant partial correlations between cognitive and social activities and hippocampal (three studies; n = 892; rz =0.07) and white matter hyperintensity volume (three studies; n = 2934; rz =-0.04). More prospective studies are needed to assess temporal associations.
AB-Gen: Antibody Library Design with Generative Pre-Trained Transformer and Deep Reinforcement Learning
Authors: Xiaopeng Xu, Tiantian Xu, Juexiao Zhou, Xingyu Liao, Ruochi Zhang, Yu Wang, Lu Zhang, Xin Gao
Journal: Genomics Proteomics & Bioinformatics (2023)

Antibody leads must fulfill multiple desirable properties to be clinical candidates. Primarily due to the low throughput in the experimental procedure, the need for such multi-property optimization causes the bottleneck in preclinical antibody discovery and development, because addressing one issue usually causes another. We developed a reinforcement learning (RL) method, named AB-Gen, for antibody library design using a generative pre-trained transformer (GPT) as the policy network of the RL agent. We showed that this model can learn the antibody space of heavy chain complementarity determining region 3 (CDRH3) and generate sequences with similar property distributions. Besides, when using human epidermal growth factor receptor-2 (HER2) as the target, the agent model of AB-Gen was able to generate novel CDRH3 sequences that fulfill multi-property constraints. Totally, 509 generated sequences were able to pass all property filters, and three highly conserved residues were identified. The importance of these residues was further demonstrated by molecular dynamics simulations, consolidating that the agent model was capable of grasping important information in this complex optimization task. Overall, the AB-Gen method is able to design novel antibody sequences with an improved success rate than the traditional propose-then-filter approach. It has the potential to be used in practical antibody design, thus empowering the antibody discovery and development process. The source code of AB-Gen is freely available at Zenodo (https://doi.org/10.5281/zenodo.7657016) and BioCode (https://ngdc.cncb.ac.cn/biocode/tools/BT007341).
FSP1: a key regulator of ferroptosis
Authors: Wentao Li, Lin Liang, Siyi Liu, Hong Yi, Yanhong Zhou
Journal: Trends in Molecular Medicine (2023)

Ferroptosis suppressor protein 1 (FSP1) is one of the main regulatory molecules of ferroptosis. FSP1 functions through the FSP1-coenzyme Q10 (CoQ10)-NAD(P)H axis and the vitamin K redox cycle. FSP1 is regulated by upstream factors, including transcription factors and noncoding RNA (ncRNA), and is subject to epigenetic modifications, which affect the progress of FSP1-related diseases. FSP1 is closely associated with the poor prognosis of malignant tumors and plays an important role in disease treatment. This review aims to provide a comprehensive understanding of the role of FSP1 in ferroptosis regulation by summarizing regulatory pathways, possible mechanisms involving FSP1, and the relationship between FSP1 and disease prognosis and treatment.
Iron‐Rich Semiconducting Polymer Dots for the Combination of Ferroptosis–Starvation and Phototherapeutic Cancer Therapy
Authors: Mingjian Chen, Yuxin Yang, Le Tang, Shuyi He, Wanni Guo, Guili Ge, Zhaoyang Zeng, Xiaoling Li, Guiyuan Li, Wei Xiong, Steven Xu Wu
Journal: Advanced Healthcare Materials (2023)

Chemodynamic therapy (CDT) has emerged as an outstanding antitumor therapeutic method due to its selectivity and utilization of tumor microenvironment. However, there are still unmet requirements to achieve a high antitumor efficiency, including the tumor accumulation of catalyst and enrichment of reactants of Fenton reaction. Here, an iron-loaded semiconducting polymer dot modified with glucose oxidase (Pdot@Fe@GOx) is reported to deliver iron ions into tumor tissues and in situ generation of hydrogen peroxide in tumors. On one hand, Pdot@Fe@GOx converts glucose to gluconic acid and hydrogen peroxide (H2 O2 ) in tumor, which not only consumes glucose of tumor cells, but also provides the H2 O2 for the following Fenton reaction. On the other hand, the Pdot@Fe@GOx delivers active iron ions in tumor to perform CDT with the combination of the generated H2 O2 . In addition, the Pdot@Fe@GOx has both photothermal and photodynamic effects under the irradiation of near-infrared laser, which can improve and compensate the CDT effect to kill cancer cells. This Pdot@Fe@GOx-based multiple-mode therapeutic strategy has successfully achieved a synergistic anticancer effect with minimal side effects and has the potential to be translated into preclinical setting for tumor therapy.
Photocurable 3D‐Printed PMBG/TCP Scaffold Coordinated with PTH (1‐34) Bidirectionally Regulates Bone Homeostasis to Accelerate Bone Regeneration
Authors: Ya Ren, Weiqing Kong, Yihao Liu, Xue Yang, Xiang Xu, Lei Qiang, Xuelian Mi, Changru Zhang, Haoyi Niu, Chengwei Wang, Jinwu Wang
Journal: Advanced Healthcare Materials (2023)

Bone defect repair remains a major clinical challenge that requires the construction of scaffolds that can regulate bone homeostasis. In this study, a photo-cured mesoporous bioactive glass (PMBG) precursor is developed as a tricalcium phosphate (TCP) agglomerant to obtain a double-phase PMBG/TCP scaffold via 3D printing. The scaffold exhibits multi-scale porous structures and large surface areas, making it a suitable carrier for the loading of parathyroid hormone (PTH) (1-34), which is used for the treatment of osteoporosis. In vitro and in vivo results demonstrate that PMBG/TCP scaffolds coordinated with PTH (1-34) can regulate bone homeostasis in a bidirectional manner to facilitate bone formation and inhibit bone resorption. Furthermore, bidirectional regulation of bone homeostasis by PTH (1-34) is achieved by inhibiting fibrogenic activation protein (FAP). Thus, PMBG/TCP scaffolds coordinated with PTH (1-34) are viable materials with considerable potential for application in the field of bone regeneration and provide an excellent solution for the design and development of clinical materials.
Nanomaterials for Disease Treatment by Modulating the Pyroptosis Pathway
Authors: Mengzhen Wang, Qinrui Fu
Journal: Advanced Healthcare Materials (2023)

Pyroptosis differs significantly from apoptosis and cell necrosis as an alternative mode of programmed cell death. Its occurrence is mediated by the gasdermin protein, leading to characteristic outcomes including cell swelling, membrane perforation, and release of cell contents. Research underscores the role of pyroptosis in the etiology and progression of many diseases, making it a focus of research intervention as scientists explore ways to regulate pyroptosis pathways in disease management. Despite numerous reviews detailing the relationship between pyroptosis and disease mechanisms, few delve into recent advancements in nanomaterials as a mechanism for modulating the pyroptosis pathway to mitigate disease effects. Therefore, there is an urgent need to fill this gap and elucidate the path for the use of this promising technology in the field of disease treatment. This review article delves into recent developments in nanomaterials for disease management through pyroptosis modulation, details the mechanisms by which drugs interact with pyroptosis pathways, and highlights the promise that nanomaterial research holds in driving forward disease treatment.
A promising tool to explore functional impairment in neurodegeneration: A systematic review of near-infrared spectroscopy in dementia.
Authors: Emilia Butters, Sruthi Srinivasan, John T. O’Brien, Li Su, Gemma Bale
Journal: Ageing Research Reviews (2023)

This systematic review aimed to evaluate previous studies which used near-infrared spectroscopy (NIRS) in dementia given its suitability as a diagnostic and investigative tool in this population. From 800 identified records which used NIRS in dementia and prodromal stages, 88 studies were evaluated which employed a range of tasks testing memory (29), word retrieval (24), motor (8) and visuo-spatial function (4), and which explored the resting state (32). Across these domains, dementia exhibited blunted haemodynamic responses, often localised to frontal regions of interest, and a lack of task-appropriate frontal lateralisation. Prodromal stages, such as mild cognitive impairment, revealed mixed results. Reduced cognitive performance accompanied by either diminished functional responses or hyperactivity was identified, the latter suggesting a compensatory response not present at the dementia stage. Despite clear evidence of alterations in brain oxygenation in dementia and prodromal stages, a consensus as to the nature of these changes is difficult to reach. This is likely partially due to the lack of standardisation in optical techniques and processing methods for the application of NIRS to dementia. Further studies are required for exploring more naturalistic settings and in a wider range of dementia subtypes.
Launch of the International Living Donor Liver Transplantation Outcomes Registry
Authors: Sebastian Staubli, Alexander Steen Grover, Benedict R H Turner, Dimitri A Raptis, Michael Spiro, Pascale Tinguely, Marina Berenguer, Mohamed Rela, Dimitri A. Raptis, Marina Berenguer, Mohamed Rela, Michael Spiro, Elizabeth Pomfret, Hiroto Egawa, Ki-Hun Kim, Prashant Bhangui, Nam J. Yi, Abhideep Chaudhary, Abhinav Humar, Abraham Shaked, Albert Chan, Alfred K.W. Chieh, Ali Jafarian, Arvinder S. Soin, Chao-Long Chen, Charles Miller, Chih-Chi Wang, Daniel Azoulay, Daniel Cherqui, Deniz Balci, Dong J. Joo, Giulano Testa, Gokhan Kabacam, Gonzalo Sapisochin, Helge Eilers, Ilgin Ozden, Jan Lerut, John P. Roberts, Jia-Hong Dong, Jiang Liu, Kim Olthoff, Kiyoshi Hasegawa, Kwan Man, Madhukar S. Patel, Mark Cattral, Massimo Malago, Mureo Kasahara, Nancy Ascher, Nazia Selzner-Malekkiani, Pooja Bhangui, Rajiv Jalan, Refaat Kamel, Rene Adam, Roberto I. Troisi, Silvio Nadalin, Sonal Asthana, Stuart A. McCluskey, Subhash Gupta, Susumu Eguchi, Terry Pan, Tiffany C.L. Wong, Vijay Vohra, Vivek Vij, Wellington Andraus, Yaman Tokat, Yuji Soejima, Andreas Mayr, Beatriz Dominguez, Elmi Muller, Karina Rando, Ashwin Rammoha, Garrett Roll, Manhal Izzy, Martin De Santibanes, Oya Andacoglu, Varvara A. Kirchner, Eleonora De Martin, Thomas Fernandez, Benedict R.H. Turner, Bhargava Chikkala, Camila Hidalgo-Salina, Emmanuel Mellul, Gulbahar Syeda, Ilya Kantsedikas, Krishnakumure Patel, Marinos Zachiotis, Meera Raja, Nidhi Reji, Nikolaos Machairas, Pascale Tinguely, Sebastian Staubli, Shahi A. Ghani, Steen Grover, Stelios-Elion Bousi, Christian E. Oberkofler
Journal: The Lancet. Gastroenterology & hepatology (2023)